Accessors for the 'counts' slot of a CountDataSet object.

Description

The counts slot holds the count data as a matrix of non-negative integer count values, one row for each observational unit (gene or the like), and one column for each sample.

Usage

## S4 method for signature 'CountDataSet'
counts(object, normalized=FALSE)
## S4 replacement method for signature 'CountDataSet,matrix'
counts(object) <- value

Arguments

Author(s)

Simon Anders, sanders@fs.tum.de

Examples

   cds <- makeExampleCountDataSet()
   head( counts( cds ) )

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
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> library(DESeq)
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
    get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
    match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
    rbind, rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unsplit

Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: locfit
locfit 1.5-9.1 	 2013-03-22
Loading required package: lattice
    Welcome to 'DESeq'. For improved performance, usability and
    functionality, please consider migrating to 'DESeq2'.
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/DESeq/counts.Rd_%03d_medium.png", width=480, height=480)
> ### Name: counts
> ### Title: Accessors for the 'counts' slot of a CountDataSet object.
> ### Aliases: counts,CountDataSet-method counts<-,CountDataSet,matrix-method
> ###   counts
> 
> ### ** Examples
> 
>    cds <- makeExampleCountDataSet()
>    head( counts( cds ) )
          A1  A2  B1  B2   B3
gene_1_F 415 518 447 239  561
gene_2_F 172 150 151 252  302
gene_3_F 422 581 128 260  667
gene_4_T 123 177 532 256 1305
gene_5_F  29  87  64  52  251
gene_6_T 245 238  26  23   60
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>